Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions

AbstractWe previously showed that single amino acid substitutions at seven positions in hemagglutinin determined major antigenic change of influenza H3N2 virus. Here, the impact of two such substitutions was tested in eleven representative H3 hemagglutinins to investigate context-dependence effects. The antigenic effect of substitutions introduced at hemagglutinin position 145 was fully independent of the amino acid context of the representative hemagglutinins. Antigenic change caused by substitutions introduced at hemagglutinin position 155 was variable and context-dependent. Our results suggest that epistatic interactions with contextual amino acids in the hemagglutinin can moderate the magnitude of antigenic change.

Download Full-text

The Impact of Single Amino Acid Substitutions in CD3γ on the CD3ϵγ Interaction and T-Cell Receptor–CD3 Complex Formation

Human Immunology ◽

10.1016/j.humimm.2006.04.015 ◽

2006 ◽

Vol 67 (8) ◽

pp. 579-588 ◽

Cited By ~ 6

Author(s):

E.A.J. Thomassen ◽

E.H.A. Dekking ◽

A. Thompson ◽

K.L. Franken ◽

Ö. Sanal ◽

...

Keyword(s):

Amino Acid ◽

T Cell ◽

Complex Formation ◽

T Cell Receptor ◽

Cell Receptor ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

The Impact

Download Full-text

Evidence for Modified Mechanisms of Chloroethene Oxidation in Pseudomonas butanovora Mutants Containing Single Amino Acid Substitutions in the Hydroxylase α-Subunit of Butane Monooxygenase

Journal of Bacteriology ◽

10.1128/jb.00189-07 ◽

2007 ◽

Vol 189 (14) ◽

pp. 5068-5074 ◽

Cited By ~ 7

Author(s):

Kimberly H. Halsey ◽

David M. Doughty ◽

Luis A. Sayavedra-Soto ◽

Peter J. Bottomley ◽

Daniel J. Arp

Keyword(s):

Amino Acid ◽

Mutant Strain ◽

Parent Compound ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

Α Subunit ◽

Mutant Strains ◽

Pseudomonas Butanovora ◽

Butane Monooxygenase ◽

The Impact

ABSTRACT The properties of oxidation of dichloroethene (DCE) and trichloroethylene (TCE) by three mutant strains of Pseudomonas butanovora containing single amino acid substitutions in the α-subunit of butane monooxygenase hydroxylase (BMOH-α) were compared to the properties of the wild-type strain (Rev WT). The rates of oxidation of three chloroethenes (CEs) were reduced in mutant strain G113N and corresponded with a lower maximum rate of butane oxidation. The rate of TCE degradation was reduced by one-half in mutant strain L279F, whereas the rates of DCE oxidation were the same as those in Rev WT. Evidence was obtained that the composition of products of CE oxidation differed between Rev WT and some of the mutant strains. For example, while Rev WT released nearly all available chlorine stoichiometrically during CE oxidation, strain F321Y released about 40% of the chlorine during 1,2-cis-DCE and TCE oxidation, and strain G113N released between 14 and 25% of the available chlorine during oxidation of DCE and 56% of the available chlorine during oxidation of TCE. Whereas Rev WT, strain L279F, and strain F321Y formed stoichiometric amounts of 1,2-cis-DCE epoxide during oxidation of 1,2-cis-DCE, only about 50% of the 1,2-cis-DCE oxidized by strain G113N was detected as the epoxide. Evidence was obtained that 1,2-cis-DCE epoxide was a substrate for butane monooxygenase (BMO) that was oxidized after the parent compound was consumed. Yet all of the mutant strains released less than 40% of the available 1,2-cis-DCE chlorine, suggesting that they have altered activity towards the epoxide. In addition, strain G113N was unable to degrade the epoxide. TCE epoxide was detected during exposure of Rev WT and strain F321Y to TCE but was not detected with strains L279F and G113N. Lactate-dependent O2 uptake rates were differentially affected by DCE degradation in the mutant strains, providing evidence that some products released by the altered BMOs reduced the impact of CE on cellular toxicity. The use of CEs as substrates in combination with P. butanovora BMOH-α mutants might allow insights into the catalytic mechanism of BMO to be obtained.

Download Full-text

Application of Evolutionary Based in Silico Methods to Predict the Impact of Single Amino Acid Substitutions in Vitelliform Macular Dystrophy

Advances in Protein Chemistry and Structural Biology ◽

10.1016/b978-0-12-800168-4.00006-8 ◽

2014 ◽

pp. 177-267 ◽

Cited By ~ 9

Author(s):

C. George Priya Doss ◽

Chiranjib Chakraborty ◽

N. Monford Paul Abishek ◽

D. Thirumal Kumar ◽

Vaishnavi Narayan

Keyword(s):

Amino Acid ◽

In Silico ◽

Single Amino Acid ◽

Macular Dystrophy ◽

Amino Acid Substitutions ◽

Vitelliform Macular Dystrophy ◽

The Impact ◽

In Silico Methods

Download Full-text

Faculty Opinions recommendation of The use of orthologous sequences to predict the impact of amino acid substitutions on protein function.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.3558956.3485081 ◽

2010 ◽

Author(s):

Alejandro Schaffer

Keyword(s):

Amino Acid ◽

Protein Function ◽

Amino Acid Substitutions ◽

The Impact

Download Full-text

Single amino acid substitutions in the reactive site of antithrombin leading to thrombosis. Congenital substitution of arginine 393 to cysteine in antithrombin Northwick Park and to histidine in antithrombin Glasgow.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)60605-2 ◽

1988 ◽

Vol 263 (12) ◽

pp. 5589-5593 ◽

Cited By ~ 4

Author(s):

H Erdjument ◽

D A Lane ◽

M Panico ◽

V Di Marzo ◽

H R Morris

Keyword(s):

Amino Acid ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

Reactive Site

Download Full-text

A Single Point Mutation, Asn16→Lys, Dictates the Temperature-Sensitivity of the Reovirus tsG453 Mutant

Viruses ◽

10.3390/v13020289 ◽

2021 ◽

Vol 13 (2) ◽

pp. 289

Author(s):

Kathleen K. M. Glover ◽

Danica M. Sutherland ◽

Terence S. Dermody ◽

Kevin M. Coombs

Keyword(s):

Amino Acid ◽

Temperature Sensitivity ◽

Reverse Genetics ◽

Core Protein ◽

Single Point ◽

Single Amino Acid ◽

Single Point Mutation ◽

Temperature Sensitive ◽

Amino Acid Substitutions ◽

Gene Encoding

Studies of conditionally lethal mutants can help delineate the structure-function relationships of biomolecules. Temperature-sensitive (ts) mammalian reovirus (MRV) mutants were isolated and characterized many years ago. Two of the most well-defined MRV ts mutants are tsC447, which contains mutations in the S2 gene encoding viral core protein σ2, and tsG453, which contains mutations in the S4 gene encoding major outer-capsid protein σ3. Because many MRV ts mutants, including both tsC447 and tsG453, encode multiple amino acid substitutions, the specific amino acid substitutions responsible for the ts phenotype are unknown. We used reverse genetics to recover recombinant reoviruses containing the single amino acid polymorphisms present in ts mutants tsC447 and tsG453 and assessed the recombinant viruses for temperature-sensitivity by efficiency-of-plating assays. Of the three amino acid substitutions in the tsG453 S4 gene, Asn16-Lys was solely responsible for the tsG453ts phenotype. Additionally, the mutant tsC447 Ala188-Val mutation did not induce a temperature-sensitive phenotype. This study is the first to employ reverse genetics to identify the dominant amino acid substitutions responsible for the tsC447 and tsG453 mutations and relate these substitutions to respective phenotypes. Further studies of other MRV ts mutants are warranted to define the sequence polymorphisms responsible for temperature sensitivity.

Download Full-text

Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies

Scientific Reports ◽

10.1038/s41598-021-92641-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Suman Pokhrel ◽

Benjamin R. Kraemer ◽

Scott Burkholz ◽

Daria Mochly-Rosen

Keyword(s):

Amino Acid ◽

Severe Disease ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

Severe Respiratory Distress ◽

S Protein ◽

Individual Sequences ◽

Natural Variants ◽

Novel Coronavirus ◽

The Individual

AbstractIn December 2019, a novel coronavirus, termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of pneumonia with severe respiratory distress and outbreaks in Wuhan, China. The rapid and global spread of SARS-CoV-2 resulted in the coronavirus 2019 (COVID-19) pandemic. Earlier during the pandemic, there were limited genetic viral variations. As millions of people became infected, multiple single amino acid substitutions emerged. Many of these substitutions have no consequences. However, some of the new variants show a greater infection rate, more severe disease, and reduced sensitivity to current prophylaxes and treatments. Of particular importance in SARS-CoV-2 transmission are mutations that occur in the Spike (S) protein, the protein on the viral outer envelope that binds to the human angiotensin-converting enzyme receptor (hACE2). Here, we conducted a comprehensive analysis of 441,168 individual virus sequences isolated from humans throughout the world. From the individual sequences, we identified 3540 unique amino acid substitutions in the S protein. Analysis of these different variants in the S protein pinpointed important functional and structural sites in the protein. This information may guide the development of effective vaccines and therapeutics to help arrest the spread of the COVID-19 pandemic.

Download Full-text